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Yorodumi- PDB-1w9o: Crystal structure of the PDZ tandem of human syntenin in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w9o | ||||||
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Title | Crystal structure of the PDZ tandem of human syntenin in complex with TNEYYV peptide | ||||||
Components |
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Keywords | CELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SCAFFOLDING PROTEIN | ||||||
Function / homology | Function and homology information interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / ionotropic glutamate receptor binding / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / cell adhesion molecule binding / ephrin receptor binding / protein sequestering activity / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / chemical synaptic transmission / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / blood microparticle / Ras protein signal transduction / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Grembecka, J. / Cierpicki, T. / Devedjiev, Y. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: The Binding of the Pdz Tandem of Syntenin to Target Proteins. Authors: Grembecka, J. / Cierpicki, T. / Devedjiev, Y. / Derewenda, U. / Kang, B.S. / Bushweller, J.H. / Derewenda, Z.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w9o.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9o.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9o ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9o | HTTPS FTP |
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-Related structure data
Related structure data | 1v1tC 1w9eC 1w9qC 1yboC 1n99S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18018.688 Da / Num. of mol.: 2 / Fragment: PDZ TANDEM, RESIDUES 113-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SDCBP, MDA9, SYCL / Plasmid: PGST-PARALLEL1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00560 #2: Protein/peptide | Mass: 787.814 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TNEYYV / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-BEZ / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 0.2M NH4CL, VAPOR DIFFUSION, SITTING DROP, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0402 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0402 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 16413 / % possible obs: 99.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 6.4 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N99 Resolution: 2.25→8 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.869 / SU B: 8.102 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
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Refine LS restraints |
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